MIT has an amazing program for System Design and Management. Dan and I are both graduates of this program. Some of the courses I would recommend include System Architecture, System Safety, and System Dynamics. Most of the content is available on OCW.

What is taught is not software-specific, but is entirely applicable to software, outside of the world of 'throw everything on the wall and see what sticks' as long as the venture capitalist can be shown growth at all costs. I wish more software developers were mindful of complexity and architecture.